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LOC113788270 Sharpr-MPRA regulatory region 12406 [ Homo sapiens (human) ]

Gene ID: 113788270, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113788270
Gene description
Sharpr-MPRA regulatory region 12406
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Dec 2018]
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Genomic context

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Location:
8p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (23070236..23070530)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (23345206..23345500)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (22927749..22928043)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984124 Neighboring gene Rho related BTB domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27100 Neighboring gene RNA, 7SL, cytoplasmic 303, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22845205-22845961 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19017 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19018 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19019 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22861268-22861793 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22861794-22862318 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:22866186-22866771 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22871840-22872604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27102 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:22876025-22876192 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22876488-22877052 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22877053-22877615 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:22885758-22886258 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:22886259-22886759 Neighboring gene TNF receptor superfamily member 10b Neighboring gene Sharpr-MPRA regulatory region 6582 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:22921484-22922683 Neighboring gene TNFRSF10B antisense RNA 1 Neighboring gene TNFRSF10B 5' regulatory region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22928365-22928864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27107 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22941919-22942800 Neighboring gene uncharacterized LOC254896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22960499-22961308 Neighboring gene TNF receptor superfamily member 10c Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22976378-22976878 Neighboring gene MPRA-validated peak6942 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19020 Neighboring gene TNF receptor superfamily member 10d Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:23002103-23002830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27108

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_062563.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    23070236..23070530
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    23345206..23345500
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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